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NEW YORK (CNNMoney) - A double whammy of federal budget cuts might force many hospitals, particularly those that serve poor or rural communities, to scale back services or even shut their doors.

The $3.6 billion in cuts this year — $2 billion from a program that sends federal dollars to hospitals that serve a high percentage of Medicaid or uninsured patients, and $1.6 billion from a drug discount program — will have the greatest effect on so-called safety net hospitals that provide medical care for all comers, no matter their ability to pay.

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The cuts are in addition to other losses of federal funds as a result of Congress' failure to reauthorize spending in 2018 on other programs affecting many hospitals. These include $1.5 billion to support community hospitals, a combined $370 million for the National Health Service Corps and Teaching Health Centers -- both of which support rural hospitals -- and $3 billion for the "Medicare extenders" program, which provides additional funding for isolated, low-volume hospitals and other rural hospitals.

"They are placing our already fragile health system in jeopardy," said Danne Howard, executive vice president of the Alabama Hospital Association. "More than 90 percent of our rural hospitals are already operating in the red. When you add further cuts to that, you are creating an extreme risk to our continued operations."

Starting Jan. 1, the Trump administration implemented a $1.6 billion cut to what is known as the 340B Drug Discount Program. Begun in 1992, the program requires drugmakers to offer deep discounts to safety net hospitals for certain drugs prescribed for Medicare patients. Those hospitals still receive full Medicare reimbursement for the drugs but can keep the difference between the discounted price and the Medicare reimbursement to plow into enhanced services to their most vulnerable patients.

Over the years, the number of health facilities qualifying for the program has grown rapidly. Between 2001 and 2011, the number of 340B facilities roughly doubled, to about 16,500 sites, according to a study published in Health Affairs in 2014. The Medicare Payment Advisory Commission said in its 2016 report to Congress that there were 2,170 340B hospitals, many of which have multiple 340B sites. In testimony before Congress in July, the Government Accountability Office reported that there are now 21,554 340B hospital sites.

But as the numbers increased, so did complaints about how the program operated. According to the Health Affairs study, more and more of the hospitals that were gaining 340B status served communities with fewer lower-income patients than the earlier 340B hospitals.

The newer 340B hospitals, the study suggested, were using their 340B status not to help poorer communities, but to push into more affluent, profitable areas.

In November, the Trump administration announced the 27 percent cut to the 340B program. Money that once went to 340B hospitals will now be distributed far more broadly, to most hospitals.

In announcing the rule change, Seema Verma, the administrator of the Centers for Medicare and Medicaid Services, said the new policy would save patients as much as $320 million in out-of-pocket prescription drug costs in 2018. Critics of the rule change are skeptical about that, noting that most Medicare beneficiaries have supplemental insurance policies that already cover those costs.

Medicaid's Disproportionate Share Hospital (DSH) program is facing even larger cuts. Created by Congress in 1981, the program is designed to compensate hospitals that provide a significant amount of medical care for which they don't receive reimbursement. In 2012, there were 2,670 such hospitals, which represented 45 percent of all hospitals, according to the Medicaid and CHIP Payment and Access Commission, a nonpartisan agency that provides analysis to Congress.

In 2017, the federal allotment for DSH payments was $12 billion, with states contributing another $9.5 billion. The commission says those payments, in the aggregate, are the difference between whether disproportionate share hospitals operate in the black or not.

Under the Affordable Care Act, the hospital program was supposed to gradually wither away, since Medicaid expansion and subsidized health insurance through the ACA's health insurance exchanges were supposed to make it unnecessary.

However, after the U.S. Supreme Court ruled in 2012 that states didn't have to expand Medicaid, Congress repeatedly delayed planned reductions to the program. In 2017, however, Congress did not vote to postpone the cuts, and they took effect Oct. 1. Unless Congress steps in, the cut to federal DSH payments in 2018 will be $2 billion, with far larger federal reductions to follow.

At the 248-bed Coosa Valley Medical Center in Tennessee, where CEP Glenn Sisk said about a quarter of the patients are on Medicaid, he anticipates that cuts to the two programs will cost his hospital between $550,000 and $650,000 this year. He said the hospital would do everything to keep the doors open, even if that meant cutting back on services or seeking another healthcare partner. He noted that Coosa Valley is the largest employer in the community, so its closure would have a devastating effect beyond the loss of medical care. "This is," he said, "an extremely serious situation for us."

The situation is also serious for Erlanger Health System, a nonprofit that operates five hospitals in the Chattanooga, Tennessee, area. Hospital officials say the expected $5 million reduction in 340B will impede the ability to care for the uninsured and underinsured.

Other hospitals mentioned the possibility of cutting back on the number of social workers, follow-ups with patients after discharge, and transportation services to help poor patients get to medical appointments.

Jeremy Alexander, interim president and CEO at the 50-bed Fort Madison Community Hospital in the southeast corner of Iowa, said the loss of 340B money could mean that the hospital will have to stop offering chemotherapy. Patients would then be faced with an hour-and-a-half drive to Iowa City.

"It's hard to swallow," he said.

The Pew Charitable Trusts funds both the Pew Research Center and Stateline.

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